This video introduces Sequencing by Expansion (SPX) technology, an innovative DNA sequencing method designed to overcome the resolution limitations of traditional techniques. SPX works by creating a surrogate "expander" molecule, significantly larger than the target DNA, which translates the DNA sequence into high-signal-to-noise reporters. This expander is synthesized using novel nucleotides (xNTPs) through a modified enzymatic DNA replication process. After synthesis and backbone expansion, the expander is deterministically threaded through a biological nanopore. A unique "translocation control element" within each reporter alters the nanopore's electrical resistance, generating distinct signals that identify the original DNA base. This highly parallel process, performed on CMOS-based sensor modules, achieves real-time sequencing rates of hundreds of millions of bases per second, offering a flexible and scalable solution for diverse genomic applications.
Sequencing by Expansion (SPX) Technology Summary
0:06 Overcoming DNA Resolution Limits: Traditional DNA sequencing struggles due to the minute 3.4 angstrom separation between DNA bases.
0:13 Introducing SPX Technology: Sequencing by Expansion (SPX) technology offers a novel solution to this challenge.
0:16 The Expander Molecule: SPX creates a "surrogate molecule" called an expander, which is more than 50 times longer than the target DNA and encodes sequence information using large, high-signal-to-noise reporters.
0:36 Novel Building Blocks (xNTPs): Expanders are synthesized using proprietary nucleotides called xNTPs (depicted as A, C, G, T).
0:43 Enzymatic Synthesis: A modified DNA replication process sequentially links xNTPs along a target DNA template using a proprietary enzymatic process, forming a double-stranded helix.
1:00 Reporter Structure: Each xNTP has a tether supporting a high-signal-to-noise reporter that mirrors the base sequence identity.
1:18 Translocation Control Element (TCE): Each reporter contains a TCE, which modulates the expander's movement during sequencing.
1:30 Correct Incorporation: Only the xNTP that correctly complements the next base on the DNA template is incorporated, transferring the DNA sequence information to the reporter sequence.
1:55 Expander Formation: After synthesis, a reagent degrades the DNA template, and cleavable bonds between xNTP bases are broken, allowing the backbone to expand, forming the final expander.
2:11 Nanopore Threading: The expander is then electrically threaded through a biological nanopore in a controlled, deterministic manner.
2:18 Signal Detection: The TCE holds each reporter within the nanopore, altering its electrical resistance to produce one of four unique signals that identify the corresponding original DNA base.
2:34 Reliable Advancement: After measurement, a short high-voltage pulse reliably advances the expander to the next reporter.
2:43 High-Throughput & Real-time Sequencing: This process is performed in parallel across millions of wells on a single CMOS-based sensor module, enabling real-time sequencing rates of hundreds of millions of bases per second.
2:59 Flexible and Scalable: Roche's innovative SPX technology is designed to be flexibly scaled to satisfy a broad range of applications, setting a new paradigm for DNA sequencing.